{"id":"https://openalex.org/W3085881182","doi":"https://doi.org/10.1093/bioinformatics/btaa782","title":"Inference of viral quasispecies with a paired de\u00a0Bruijn\u00a0graph","display_name":"Inference of viral quasispecies with a paired de\u00a0Bruijn\u00a0graph","publication_year":2020,"publication_date":"2020-09-02","ids":{"openalex":"https://openalex.org/W3085881182","doi":"https://doi.org/10.1093/bioinformatics/btaa782","mag":"3085881182","pmid":"https://pubmed.ncbi.nlm.nih.gov/32926162"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa782","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa782","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"http://hdl.handle.net/10138/341190","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101567995","display_name":"Borja Freire","orcid":"https://orcid.org/0000-0003-0317-5482"},"institutions":[{"id":"https://openalex.org/I11019714","display_name":"Universidade da Coru\u00f1a","ror":"https://ror.org/01qckj285","country_code":"ES","type":"education","lineage":["https://openalex.org/I11019714"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Borja Freire","raw_affiliation_strings":["Department of Computer Science and Information Technologies, Facultade de Inform\u00e1tica, Universidade da Coru\u00f1a , Centro de investigaci\u00f3n CITIC, A Coru\u00f1a, Spain"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Information Technologies, Facultade de Inform\u00e1tica, Universidade da Coru\u00f1a , Centro de investigaci\u00f3n CITIC, A Coru\u00f1a, Spain","institution_ids":["https://openalex.org/I11019714"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085109336","display_name":"Susana Ladra","orcid":"https://orcid.org/0000-0003-4616-0774"},"institutions":[{"id":"https://openalex.org/I11019714","display_name":"Universidade da Coru\u00f1a","ror":"https://ror.org/01qckj285","country_code":"ES","type":"education","lineage":["https://openalex.org/I11019714"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Susana Ladra","raw_affiliation_strings":["Department of Computer Science and Information Technologies, Facultade de Inform\u00e1tica, Universidade da Coru\u00f1a , Centro de investigaci\u00f3n CITIC, A Coru\u00f1a, Spain"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Information Technologies, Facultade de Inform\u00e1tica, Universidade da Coru\u00f1a , Centro de investigaci\u00f3n CITIC, A Coru\u00f1a, Spain","institution_ids":["https://openalex.org/I11019714"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027984124","display_name":"Jos\u00e9 R. Param\u00e1","orcid":"https://orcid.org/0000-0002-8727-0980"},"institutions":[{"id":"https://openalex.org/I11019714","display_name":"Universidade da Coru\u00f1a","ror":"https://ror.org/01qckj285","country_code":"ES","type":"education","lineage":["https://openalex.org/I11019714"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Jose R Param\u00e1","raw_affiliation_strings":["Department of Computer Science and Information Technologies, Facultade de Inform\u00e1tica, Universidade da Coru\u00f1a , Centro de investigaci\u00f3n CITIC, A Coru\u00f1a, Spain"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Information Technologies, Facultade de Inform\u00e1tica, Universidade da Coru\u00f1a , Centro de investigaci\u00f3n CITIC, A Coru\u00f1a, Spain","institution_ids":["https://openalex.org/I11019714"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5091190630","display_name":"Leena Salmela","orcid":"https://orcid.org/0000-0002-0756-543X"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]},{"id":"https://openalex.org/I32943570","display_name":"Helsinki Institute for Information Technology","ror":"https://ror.org/05kph4940","country_code":"FI","type":"facility","lineage":["https://openalex.org/I133731052","https://openalex.org/I32943570","https://openalex.org/I9927081"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Leena Salmela","raw_affiliation_strings":["Department of Computer Science, Helsinki Institute for Information Technology, University of Helsinki , Helsinki, Finland"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Helsinki Institute for Information Technology, University of Helsinki , Helsinki, Finland","institution_ids":["https://openalex.org/I32943570","https://openalex.org/I133731052"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5027984124"],"corresponding_institution_ids":["https://openalex.org/I11019714"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.0837,"has_fulltext":false,"cited_by_count":19,"citation_normalized_percentile":{"value":0.86272264,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"37","issue":"4","first_page":"473","last_page":"481"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11048","display_name":"Bacteriophages and microbial interactions","score":0.9970999956130981,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11048","display_name":"Bacteriophages and microbial interactions","score":0.9970999956130981,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9965000152587891,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11135","display_name":"Virology and Viral Diseases","score":0.9811000227928162,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/viral-quasispecies","display_name":"Viral quasispecies","score":0.7754378318786621},{"id":"https://openalex.org/keywords/de-bruijn-graph","display_name":"De Bruijn graph","score":0.7460871934890747},{"id":"https://openalex.org/keywords/de-bruijn-sequence","display_name":"De Bruijn sequence","score":0.7368249893188477},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.6185560822486877},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5651213526725769},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5079393982887268},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.42360636591911316},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.36816519498825073},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3494681417942047},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.27517420053482056},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.23526862263679504},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.22332200407981873},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2098715603351593},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.18521049618721008},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.09130913019180298}],"concepts":[{"id":"https://openalex.org/C14500911","wikidata":"https://www.wikidata.org/wiki/Q3413375","display_name":"Viral quasispecies","level":4,"score":0.7754378318786621},{"id":"https://openalex.org/C20218877","wikidata":"https://www.wikidata.org/wiki/Q3066095","display_name":"De Bruijn graph","level":3,"score":0.7460871934890747},{"id":"https://openalex.org/C170320093","wikidata":"https://www.wikidata.org/wiki/Q1953457","display_name":"De Bruijn sequence","level":2,"score":0.7368249893188477},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6185560822486877},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5651213526725769},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5079393982887268},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.42360636591911316},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.36816519498825073},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3494681417942047},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.27517420053482056},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.23526862263679504},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.22332200407981873},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2098715603351593},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.18521049618721008},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.09130913019180298}],"mesh":[{"descriptor_ui":"D000074704","descriptor_name":"Quasispecies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000074704","descriptor_name":"Quasispecies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000074704","descriptor_name":"Quasispecies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaa782","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa782","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:32926162","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32926162","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:helda.helsinki.fi:10138/341190","is_oa":true,"landing_page_url":"http://hdl.handle.net/10138/341190","pdf_url":null,"source":{"id":"https://openalex.org/S4210213322","display_name":"Ty\u00f6v\u00e4entutkimus Vuosikirja","issn_l":"0784-1272","issn":["0784-1272","1459-7780"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"}],"best_oa_location":{"id":"pmh:oai:helda.helsinki.fi:10138/341190","is_oa":true,"landing_page_url":"http://hdl.handle.net/10138/341190","pdf_url":null,"source":{"id":"https://openalex.org/S4210213322","display_name":"Ty\u00f6v\u00e4entutkimus Vuosikirja","issn_l":"0784-1272","issn":["0784-1272","1459-7780"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2069040777","display_name":null,"funder_award_id":"323233","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"},{"id":"https://openalex.org/G295869355","display_name":null,"funder_award_id":"ED431C 2017/58","funder_id":"https://openalex.org/F4320326655","funder_display_name":"Xunta de Galicia"},{"id":"https://openalex.org/G3458627852","display_name":null,"funder_award_id":"IN848D-2017-2350417","funder_id":"https://openalex.org/F4320326655","funder_display_name":"Xunta de Galicia"},{"id":"https://openalex.org/G6120476676","display_name":"Complete and accurate reconstruction of biological sequences","funder_award_id":"308030","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"},{"id":"https://openalex.org/G6974483010","display_name":null,"funder_award_id":"308030","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"},{"id":"https://openalex.org/G7482227533","display_name":null,"funder_award_id":"314170","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"},{"id":"https://openalex.org/G7651122875","display_name":null,"funder_award_id":"IN852A 2018/14","funder_id":"https://openalex.org/F4320326655","funder_display_name":"Xunta de Galicia"},{"id":"https://openalex.org/G8373554017","display_name":null,"funder_award_id":"ED431G/01","funder_id":"https://openalex.org/F4320326655","funder_display_name":"Xunta de Galicia"}],"funders":[{"id":"https://openalex.org/F4320321108","display_name":"Academy of Finland","ror":"https://ror.org/05k73zm37"},{"id":"https://openalex.org/F4320326655","display_name":"Xunta de Galicia","ror":"https://ror.org/0181xnw06"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":29,"referenced_works":["https://openalex.org/W1993577356","https://openalex.org/W2020939898","https://openalex.org/W2025161234","https://openalex.org/W2027969303","https://openalex.org/W2036897871","https://openalex.org/W2065256070","https://openalex.org/W2068743009","https://openalex.org/W2073918065","https://openalex.org/W2105067980","https://openalex.org/W2105757606","https://openalex.org/W2120902911","https://openalex.org/W2128711701","https://openalex.org/W2134007392","https://openalex.org/W2160177274","https://openalex.org/W2163326395","https://openalex.org/W2175526948","https://openalex.org/W2336086067","https://openalex.org/W2461605911","https://openalex.org/W2524622036","https://openalex.org/W2599417231","https://openalex.org/W2789208418","https://openalex.org/W2795049082","https://openalex.org/W2895878640","https://openalex.org/W2949491511","https://openalex.org/W2950774292","https://openalex.org/W2951613337","https://openalex.org/W2952626522","https://openalex.org/W3094571539","https://openalex.org/W6703155622"],"related_works":["https://openalex.org/W2562683361","https://openalex.org/W3087469195","https://openalex.org/W2354744388","https://openalex.org/W3125399386","https://openalex.org/W2949121831","https://openalex.org/W1908987670","https://openalex.org/W2756186577","https://openalex.org/W2735897904","https://openalex.org/W3215786367","https://openalex.org/W3085881182"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":9},{"year":2021,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
